---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2009-05-20 05:07:59+00:00
layout: post
slug: dna-methylation-test-gigas-site-gdna-bb-dh-from-20090515
title: DNA Methylation Test - Gigas site gDNA (BB & DH) from 20090515
categories:
  - 2009
  - Miscellaneous
tags:
  - BB
  - Crassostrea gigas
  - DH
  - gDNA
  - graphs
  - methylation
  - Pacific oyster
  - plate reader
---

Used BB & DH samples #11-17 for procedure. Followed Epigentek's protocol. [My calcs for dilutions/solutions needed are here](https://eagle.fish.washington.edu/Arabidopsis/Notebook%20Workup%20Files/20090519-01.jpg). All solutions were made fresh before using, except for Diluted GU1 which was made at the beginning of the procedure and stored on ice in a 50mL conical wrapped in aluminum foil. Used 100ng total (50ng/uL) of each sample gDNA. No standards for a standard curve based on speaking with Mac.

<table class="wiki_table mceItemTable" >
<tbody >
<tr >

<td >**WELL**
</td>

<td >**SAMPLE**
</td>

<td >**WELL**
</td>

<td >**SAMPLE**
</td>
</tr>
<tr >

<td >A01
</td>

<td >BB11
</td>

<td >A02
</td>

<td >DH11
</td>
</tr>
<tr >

<td >B01
</td>

<td >BB12
</td>

<td >B02
</td>

<td >DH12
</td>
</tr>
<tr >

<td >C01
</td>

<td >BB13
</td>

<td >C02
</td>

<td >DH13
</td>
</tr>
<tr >

<td >D01
</td>

<td >BB14
</td>

<td >D02
</td>

<td >DH14
</td>
</tr>
<tr >

<td >E01
</td>

<td >BB15
</td>

<td >E02
</td>

<td >DH15
</td>
</tr>
<tr >

<td >F01
</td>

<td >BB16
</td>

<td >F02
</td>

<td >DH16
</td>
</tr>
<tr >

<td >G01
</td>

<td >BB17
</td>

<td >G02
</td>

<td >DH17
</td>
</tr>
<tr >

<td >H01
</td>

<td >Pos. Control
</td>

<td >H02
</td>

<td >Blank
</td>
</tr>
</tbody>
</table>

![](https://eagle.fish.washington.edu/Arabidopsis/20090519%20gigas%20methylation%20BB%20vs%20DH%20graph.jpg)

Results: Above is the graph of the results. Although it's only a small difference between the two sites, it is statistically significant. [The calcs for this graph can be found here (Excel file)(https://eagle.fish.washington.edu/Arabidopsis/Notebook%20Workup%20Files/20090519%20Gigas%20DNA%20methylation%20workup%20SJW.xls). It should be noted that this graph was generated using estimated values from the standard curve provided in the manufacturer's protocol. This was done because 1) I did not run standards to generate my own curve and 2) calculating the "% methylation" not using the formula that utilizes the standard curve was giving ridiculously high values (e.g. 350%).

Here is the raw data generated by the plate reader for a [1s read (Excel file)(https://eagle.fish.washington.edu/Arabidopsis/Notebook%20Workup%20Files/20090519%20gDNA%20Methylation%201s%20SJW.xls) and [a 0.1s (Excel file) read](http://eagle.fish.washington.edu/Arabidopsis/Notebook%20Workup%20Files/20090519%20gDNA%20Methylation%200.1s%20SJW.xls). Both reads have nearly identical values.